What does Pac-man going rogue have to do with DNA repair?

If I ask you to tell me what DNA looks like, I am sure the first image to be pictured is that iconic double helix structure, floating and twisting slowly in the air, consisting of a long backbone with bases sticking out into the middle acting as the code itself. Its discovery revolutionised the world and sparked huge scientific advancement. With this advancement came the realisation that DNA – the very code that allows us to exist as humans – needs constant protection and repair of damage. Without efficient DNA repair methods, cells can develop into that terrifying C word – Cancer.

There are many routes by which DNA can be repaired, but the one I care most about is called Base Excision Repair, or BER. BER is initiated by a specific kind of enzyme known as a glycosylase. This enzyme is able to recognise that the DNA code has been damaged, and essentially chomps away at it to remove that damaged bit of code, leaving behind the backbone – like pac-man gone rogue.

Other enzymes then follow to fill in the gap left behind with the correct version of the removed base restoring your DNA back to its (hopefully) non-cancerous state. The specific glycosylase enzyme I’m looking at is called Alkyladenine DNA glycosylase. It’s a mouthful so let’s just call it AAG (I dare you to say it out loud and not giggle).

How does AAG work? A) The typical structure of a strand of DNA the pentose sugar phosphate backbone with the DNA bases (rectangles) sticking out into the centre. B) A DNA strand with a damaged DNA base (red triangle) with AAG (Yellow) recognising it and chomping it away.

AAG is interesting in that as a DNA repair enzyme, you would naturally think if a cell has more AAG in it, then that cell’s DNA must be more protected! The more DNA repair the better, surely?

Apparently not.

If there is too much AAG in the nucleus where our DNA is found, then cells are even more likely to die when treated with chemicals that cause DNA damage. What they found was that after AAG goes all pac-man and removes that damaged base, the left-over half-eaten DNA that remains before the DNA gets fully repaired is super toxic to the cell and can cause it to die, especially when there is lots of that left-over, half-eaten DNA. In other words, the pac-man-like effect of AAG causes more damage to cells when there is too much of AAG around.

We also know that there is DNA in the mitochondria of a cell. Not as much as in the nucleus, but we know the DNA there is just as important. And increasing the amount of AAG in the mitochondria actually kills cells even when there isn’t any DNA damage being caused by a chemical! So, what on earth is happening there? There is another protein in the mitochondria called mtSSB which is capable of attaching to mitochondrial DNA and AAG to protect the vulnerable mitochondrial DNA from being chomped at by AAG. My hypothesis is that when you increase AAG in the mitochondria, mtSSB can’t cope with that sudden increase and isn’t able to fully protect that DNA anymore, causing cell death to even greater extents.

As part of my MSci research, I will be artificially changing the levels of AAG or mtSSB in cells and observing how those changes affect the health of the cell. I think that this will help us target treatments for cancer patients. If we can identify whether changes in the amount of pac-man activity in the cell makes cancer more likely to die from DNA damage, then we might be able to predict how patients respond to different chemotherapies, making treatment more effective! Now we just have to wait and see.

Further Reading:

  1. Balancing repair and tolerance of DNA damage caused by alkylating agents (2012) Fu, D., Calvo, J. A., and Samson, L. D. Nature Reviews Cancer, 12, pp.104-20. DOI: 10.1038/nrc3185
  2. AAG DNA Glycosylase Promotes Alkylation-Induced Tissue Damage Mediated by Parp1 (2013) Calvo, J. A., Moroski-Erkul, C. A., Lake, A., Eichinger, L. W., Shah, D., Jhun, I., Limsirichai, P., Bronson, R. T. Christiani, D. C., Meira, L. B., and Samson, L. D. PLOS Genetics, 9;4. DOI: 10.1371/journal.pgen.1003413
  3. Imbalancing the DNA Base Excision Repair Pathway in the Mitochondria; Targeting and Overexpressing N-Methylpurine DNA Glycosylase in Mitochondria Leads to Enhanced Cell Killing (2003) Fishel, M. L., Seo, Y.  R., Smith, M. L., and Kelley, M. R. Cancer Research, 63, pp. 608-15. Available at: https://cancerres.aacrjournals.org/content/63/3/608
  4. Alkyladenine DNA glycosylase (AAG) localizes to the mitochondria and interacts with mitochondrial single-stranded binding protein (mtSSB) (2013) Van Loon, B., and Samson, L. D. DNA Repair, 12;3, pp. 177-87. DOI: 10.1016/j.dnarep.2012.11.009
  5. Mitochondrial DNA damage is more extensive and persists longer than nuclear DNA damage in human cells following oxidative stress (1997) Yakes, F. M., and van Houten, B. PNAS, 94, pp. 514-9. DOI: 10.1073/pnas.94.2.514